Mon Oct 10 12:12:44 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 12:12:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7614973 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 8.905001 54.98900 ymin,ymax (A): -8.872000 35.88500 zmin,zma (A): -3.076000 43.67400 x,y,z range (A): 46.08400 44.75700 46.75000 scale (grids/A): 0.7614973 object centre (A): 31.94700 13.50650 20.29900 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.55728 90.63805 90.16708 assigned negative charge : -323.3720 centred at (gu) : 89.56514 90.73433 90.33858 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8397 nv = 96 ne = 84 npr = 44123 no. pairs analyzed = 44123 no. exposed pairs = 2688 no. arc points = 18901 no. surface atoms = 909 nbur = 1208 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 666 mr = 4687 m= 7 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 158 time to turn everything in is 0.3100000 number of dielectric boundary points 4229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1452 ## 109 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8690 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0021729E-08 -4.5968167E-07 midg,1,midg; midg,igrid,midg -2.0744126E-08 -3.6453019E-07 1,midg,midg; igrid,midg,midg -1.7248090E-07 -1.7055386E-07 gauss-seidel spectral radius is 0.9910098 estimated iterations to convergence 86 setup time was (sec) 0.7900000 now iterating at: 12:12:45 rms-change max change #iterations 0.2712736 34.68540 at 10iterations 3.8322087E-02 4.386538 at 20iterations 5.4947864E-03 0.6913052 at 30iterations 7.8276324E-04 9.2782021E-02 at 40iterations 1.1268715E-04 1.2725830E-02 at 50iterations finished qdiffx linear iterations at : 12:12:53 total time elapsed so far: 8.520000 # loops : 50 mean,max change (kT/e) : 1.1268715E-04 1.2725830E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 12:12:54 8.711u 0.682s 0:09.94 94.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 12:12:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.284492 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 8.905001 54.98900 ymin,ymax (A): -8.872000 35.88500 zmin,zma (A): -3.076000 43.67400 x,y,z range (A): 46.08400 44.75700 46.75000 scale (grids/A): 2.284492 object centre (A): 31.94700 13.50650 20.29900 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.67197 91.91392 90.50138 assigned negative charge : -323.3720 centred at (gu) : 88.69569 92.20300 91.01563 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18901 grid for indexing accessible points = 1.400000 m= 36065 mr = 60075 m= 8369 mr = 27674 m= 1023 mr = 5979 m= 40 mr = 612 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 4608 time to turn everything in is 0.8800000 number of dielectric boundary points 38518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 15785 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7614973 object centre at (A) : 31.94700 13.50650 20.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4475913E-03 -0.1415356 midg,1,midg; midg,igrid,midg -2.7687861E-02 -5.5379484E-02 1,midg,midg; igrid,midg,midg -2.5315974E-02 -3.3053961E-02 gauss-seidel spectral radius is 0.9989741 estimated iterations to convergence 247 setup time was (sec) 1.440000 now iterating at: 12:12:56 rms-change max change #iterations 5.342401 230.8969 at 10iterations 2.758435 88.66468 at 20iterations 1.423118 37.73086 at 30iterations 0.7365504 20.19015 at 40iterations 0.3809148 10.72287 at 50iterations 0.1973204 5.779728 at 60iterations 0.1023386 2.652081 at 70iterations 5.3061694E-02 1.379242 at 80iterations 2.7396601E-02 0.7460518 at 90iterations 1.4209866E-02 0.3986187 at 100iterations 7.3566437E-03 0.1912737 at 110iterations 3.7869962E-03 9.9935532E-02 at 120iterations finished qdiffx linear iterations at : 12:13:16 total time elapsed so far: 20.88000 # loops : 120 mean,max change (kT/e) : 3.7869962E-03 9.9935532E-02 energy calculations done at 20.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.07000 DelPhi exited at 12:13:16 21.072u 0.868s 0:22.47 97.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 12:13:16 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.426738 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 8.905001 54.98900 ymin,ymax (A): -8.872000 35.88500 zmin,zma (A): -3.076000 43.67400 x,y,z range (A): 46.08400 44.75700 46.75000 scale (grids/A): 3.426738 object centre (A): 31.94700 13.50650 20.29900 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.00787 92.87090 90.75206 assigned negative charge : -323.3720 centred at (gu) : 88.04346 93.30450 91.52347 start vw surface at 0.1300000 fill in re-entrant regions at 1.120000 boundary points on vw surface= 200707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18901 grid for indexing accessible points = 1.400000 m= 108930 mr = 144237 m= 48708 mr = 90715 m= 16445 mr = 40876 m= 3925 mr = 13265 m= 689 mr = 3046 m= 39 mr = 510 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 15409 time to turn everything in is 2.660000 number of dielectric boundary points 86783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.850000 number of grid points assigned charge 15824 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.284492 object centre at (A) : 31.94700 13.50650 20.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8889843E-02 -1.389992 midg,1,midg; midg,igrid,midg -0.2412983 -0.2582467 1,midg,midg; igrid,midg,midg -0.2977011 -0.4297204 gauss-seidel spectral radius is 0.9993320 estimated iterations to convergence 305 setup time was (sec) 3.070000 now iterating at: 12:13:20 rms-change max change #iterations 11.38759 289.6747 at 10iterations 6.737972 110.3818 at 20iterations 4.002951 88.92542 at 30iterations 2.370169 41.56450 at 40iterations 1.404602 23.45516 at 50iterations 0.8286899 13.21046 at 60iterations 0.4905045 7.604001 at 70iterations 0.2901597 4.603668 at 80iterations 0.1716160 2.687069 at 90iterations 0.1011430 1.630046 at 100iterations 5.9710193E-02 1.066124 at 110iterations 3.5250600E-02 0.5147896 at 120iterations 2.0820566E-02 0.3311392 at 130iterations 1.2309887E-02 0.2008524 at 140iterations 7.2541540E-03 0.1103992 at 150iterations 4.3001310E-03 6.7581177E-02 at 160iterations 2.5339853E-03 3.9396286E-02 at 170iterations 1.4998598E-03 2.3437500E-02 at 180iterations finished qdiffx linear iterations at : 12:13:50 total time elapsed so far: 32.68000 # loops : 180 mean,max change (kT/e) : 1.4998598E-03 2.3437500E-02 energy calculations done at 32.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.86000 DelPhi exited at 12:13:50 32.863u 0.774s 0:33.99 98.9% 0+0k 0+0io 0pf+0w